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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ), 'gf_id' => 'HOM05D001184', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001184' ), 'data_identifier' => 'HOM05D001184', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001184', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p08440' => 'bna', 'A05p01840' => 'bna', 'A08p06650' => 'bna', 'A09p52320' => 'bna', 'Aa31LG10G14200' => 'aar', 'Aa31LG3G1460' => 'aar', 'Aa31LG4G12540' => 'aar', 'Aa31LG9G3730' => 'aar', 'Aa31LG9G3740' => 'aar', 'Aa31LG9G3750' => 'aar', 'Aa31LG9G3760' => 'aar', 'Aa31LG9G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1191' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3561' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3910' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2232' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.629' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2348' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2800' => 'aag', 'Actinidia03535' => 'ach', 'Actinidia03536' => 'ach', 'Actinidia11423' => 'ach', 'Actinidia13646' => 'ach', 'Actinidia29359' => 'ach', 'Actinidia31465' => 'ach', 'Actinidia31466' => 'ach', 'Actinidia39243' => 'ach', 'Ah.01g012860' => 'amhyb', 'Ah.07g201900' => 'amhyb', 'Ah.07g203410' => 'amhyb', 'Ah.12g064390' => 'amhyb', 'Ah.13g069000' => 'amhyb', 'Ah.13g078050' => 'amhyb', 'Ah.13g078060' => 'amhyb', 'Ah.16g102160' => 'amhyb', 'AL1G21770' => 'aly', 'AL2G17960' => 'aly', 'AL4G38530' => 'aly', 'AL5G42160' => 'aly', 'AL7G42740' => 'aly', 'Aqoxy1G00518' => 'aox', 'Aqoxy2G00714' => 'aox', 'Aqoxy5G01118' => 'aox', 'Aqoxy5G03290' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1BRL89' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.28RW3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6FVUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6K76F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X99BTJ' => 'arhy', 'AT2G40660' => 'ath', 'AT3G59980' => 'ath', 'AT4G13780' => 'ath', 'AT5G02680' => 'ath', 'ATR0582G097' => 'atr', 'ATR0987G002' => 'atr', 'ATR0987G004' => 'atr', 'ATR1127G003' => 'atr', 'Atru.BG.63.p' => 'acertr', 'Atru.chr12.216' => 'acertr', 'Atru.chr13.1877' => 'acertr', 'Atru.chr4.1616' => 'acertr', 'AUR62002513' => 'cqu', 'AUR62018575' => 'cqu', 'AUR62020841' => 'cqu', 'AUR62023681' => 'cqu', 'AUR62024937' => 'cqu', 'AUR62029185' => 'cqu', 'AUR62030607' => 'cqu', 'AUR62034373' => 'cqu', 'AUR62035918' => 'cqu', 'AUR62037694' => 'cqu', 'BcaB02g08652' => 'bca', 'BcaB07g33456' => 'bca', 'BcaB07g33518' => 'bca', 'BcaC02g09391' => 'bca', 'BcaC02g12728' => 'bca', 'BcaC07g37333' => 'bca', 'BcaC07g40403' => 'bca', 'BcaC07g40536' => 'bca', 'BcaC09g50472' => 'bca', 'BcaNung00123' => 'bca', 'BolC1t02445H' => 'bol', 'BolC4t21862H' => 'bol', 'BolC4t25796H' => 'bol', 'BolC7t42786H' => 'bol', 'BolC8t47619H' => 'bol', 'BolC8t51102H' => 'bol', 'BraA04t16533Z' => 'bra', 'BraA05t19182Z' => 'bra', 'BraA08t32681Z' => 'bra', 'BraA09t38308Z' => 'bra', 'BraA09t40661Z' => 'bra', 'C01p25010' => 'bna', 'C04p02140' => 'bna', 'C04p42150' => 'bna', 'C07p22130' => 'bna', 'C08p07710' => 'bna', 'C08p34980' => 'bna', 'CAN.G17.14' => 'can', 'CAN.G246.2' => 'can', 'CAN.G305.8' => 'can', 'CAN.G50.12' => 'can', 'CANSAT01G1772' => 'cansat', 'CANSAT56G1814' => 'cansat', 'CANSAT56G3362' => 'cansat', 'CANSAT78G2277' => 'cansat', 'CARHR054020' => 'chi', 'CARHR135770' => 'chi', 'CARHR170300' => 'chi', 'CARHR219660' => 'chi', 'CARHR219670' => 'chi', 'Carub.0004s2295' => 'cru', 'Carub.0005s2671' => 'cru', 'Carub.0007s2868' => 'cru', 'Carub.0007s3400' => 'cru', 'Ca_04924_v3' => 'car', 'Ca_16863_v3' => 'car', 'Ca_27238_v3' => 'car', 'CBR_g16052' => 'cbr', 'CBR_g55333' => 'cbr', 'Cc02_g05330' => 'ccan', 'Cc03_g08090' => 'ccan', 'Cc03_g16240' => 'ccan', 'Cc03_g16250' => 'ccan', 'Cc03_g16270' => 'ccan', 'CDE02G1448' => 'cde', 'CDE02G1690' => 'cde', 'CDE02G3951' => 'cde', 'CDE02G4139' => 'cde', 'CDE06G0050' => 'cde', 'CDE08G1095' => 'cde', 'CDE12G0518' => 'cde', 'Cfa001206' => 'cfa', 'Cfa002591' => 'cfa', 'Cfa008543' => 'cfa', 'Cfa022327' => 'cfa', 'Cfa024387' => 'cfa', 'Cfa025635' => 'cfa', 'Ciclev10004343m.g' => 'ccl', 'Ciclev10021676m.g' => 'ccl', 'Ciclev10024095m.g' => 'ccl', 'Ciclev10031719m.g' => 'ccl', 'CiPaw.02G065500' => 'cil', 'CiPaw.02G126300' => 'cil', 'CiPaw.03G146700' => 'cil', 'CiPaw.04G147400' => 'cil', 'ClCG04G002910' => 'cla', 'ClCG06G008040' => 'cla', 'ClCG07G005160' => 'cla', 'COL.COLO4_19421' => 'col', 'COL.COLO4_19508' => 'col', 'COL.COLO4_20192' => 'col', 'Cpa.g.sc19.53' => 'cpa', 'Cpa.g.sc8.130' => 'cpa', 'Cpa.g.sc83.20' => 'cpa', 'Cre01.g046652' => 'cre', 'Cre02.g087950' => 'cre', 'Cre03.g145967' => 'cre', 'Cre07.g326950' => 'cre', 'Cre08.g364650' => 'cre', 'CsaV3_2G011140' => 'csa', 'CsaV3_4G029850' => 'csa', 'CsaV3_5G011010' => 'csa', 'CSS0000282' => 'camsi', 'CSS0000981' => 'camsi', 'CSS0006835' => 'camsi', 'CSS0010950' => 'camsi', 'CSS0016595' => 'camsi', 'CSS0018170' => 'camsi', 'CSS0018804' => 'camsi', 'CSS0021172' => 'camsi', 'CSS0024612' => 'camsi', 'CSS0027515' => 'camsi', 'CSS0035920' => 'camsi', 'CSS0036533' => 'camsi', 'CSS0043546' => 'camsi', 'DCAR_018640' => 'dca', 'DCAR_020150' => 'dca', 'DCAR_023795' => 'dca', 'DCAR_023870' => 'dca', 'DCAR_026633' => 'dca', 'Dinv12661' => 'din', 'Dinv24736' => 'din', 'Dinv34490' => 'din', 'Dinv38206' => 'din', 'Duzib114G1043' => 'dzi', 'Duzib128G0215' => 'dzi', 'Duzib212G0797' => 'dzi', 'Duzib268G0787' => 'dzi', 'ECA233G0243' => 'eca', 'ECA236G4007' => 'eca', 'ECA238G2482' => 'eca', 'ECA246G1833' => 'eca', 'ECA246G4496' => 'eca', 'ECA247G2182' => 'eca', 'EL10Ac1g00236' => 'bvu', 'EL10Ac2g02652' => 'bvu', 'EL10Ac3g06196' => 'bvu', 'EL10Ac3g07475' => 'bvu', 'EL10Ac6g14498' => 'bvu', 'EL10Ac8g19256' => 'bvu', 'Eucgr.H00043' => 'egr', 'Eucgr.J00111' => 'egr', 'FAN01G0629' => 'fan', 'FAN03G2754' => 'fan', 'FAN04G2014' => 'fan', 'FAN06G0458' => 'fan', 'FAN07G0119' => 'fan', 'FAN10G0995' => 'fan', 'FAN12G0346' => 'fan', 'FAN12G0873' => 'fan', 'FAN17G0017' => 'fan', 'FAN22G0763' => 'fan', 'FAN23G2940' => 'fan', 'FAN26G1600' => 'fan', 'FAN28G2093' => 'fan', 'FvH4_1g00030' => 'fve', 'FvH4_4g13560' => 'fve', 'FvH4_4g36101' => 'fve', 'FvH4_4g36103' => 'fve', 'FvH4_7g25960' => 'fve', 'Glyma.04G222900' => 'gma', 'Glyma.06G142400' => 'gma', 'Glyma.09G158400' => 'gma', 'Glyma.09G227400' => 'gma', 'Glyma.12G009400' => 'gma', 'Glyma.12G018300' => 'gma', 'Glyma.12G018400' => 'gma', 'Glyma.13G000200' => 'gma', 'Gohir.A09G206100' => 'ghi', 'Gohir.A10G180150' => 'ghi', 'Gohir.A10G192100' => 'ghi', 'Gohir.D09G199700' => 'ghi', 'Gohir.D10G187100' => 'ghi', 'Gohir.D10G199900' => 'ghi', 'Gorai.006G223400' => 'gra', 'Gorai.011G209900' => 'gra', 'Gorai.011G224100' => 'gra', 'GSVIVG01009512001' => 'vvi', 'GSVIVG01009513001' => 'vvi', 'GSVIVG01012990001' => 'vvi', 'GSVIVG01020924001' => 'vvi', 'GSVIVG01021990001' => 'vvi', 'GSVIVG01032669001' => 'vvi', 'GSVIVG01038277001' => 'vvi', 'GSVIVG01038361001' => 'vvi', 'HanXRQChr02g0059041' => 'han', 'HanXRQChr05g0143251' => 'han', 'HanXRQChr07g0189471' => 'han', 'HanXRQChr09g0251041' => 'han', 'HanXRQChr11g0340281' => 'han', 'HanXRQChr14g0460711' => 'han', 'HanXRQChr15g0488241' => 'han', 'Haze_03548' => 'cav', 'Haze_11089' => 'cav', 'Haze_17360' => 'cav', 'Haze_24834' => 'cav', 'Haze_24837' => 'cav', 'Haze_26590' => 'cav', 'Haze_27406' => 'cav', 'Hma1.2p1_0187F.1_g082410' => 'hma', 'Hma1.2p1_1125F.1_g259610' => 'hma', 'HPP92_007221' => 'vpl', 'HPP92_015593' => 'vpl', 'HPP92_020335' => 'vpl', 'HPP92_023535' => 'vpl', 'Hund13448' => 'sun', 'Hund18999' => 'sun', 'Hund21466' => 'sun', 'Hund22665' => 'sun', 'Lalb_Chr01g0000441' => 'lal', 'Lalb_Chr01g0000971' => 'lal', 'Lalb_Chr08g0239191' => 'lal', 'Lalb_Chr11g0067771' => 'lal', 'Lalb_Chr19g0139901' => 'lal', 'Lj1A88G44' => 'lonja', 'Lj1A967T43' => 'lonja', 'Lj1A968G50' => 'lonja', 'Lj1g0025527' => 'lja', 'Lj2A405G34' => 'lonja', 'Lj2A407G27' => 'lonja', 'Lj2A677T26' => 'lonja', 'Lj2C407T13' => 'lonja', 'Lj3g0023071' => 'lja', 'Lj3g0023242' => 'lja', 'Lj9P427T28' => 'lonja', 'Lsat_1_v5_gn_1_91420' => 'lsa', 'Lsat_1_v5_gn_2_126320' => 'lsa', 'Lsat_1_v5_gn_2_46341' => 'lsa', 'Lsat_1_v5_gn_4_149740' => 'lsa', 'Lsat_1_v5_gn_6_101301' => 'lsa', 'Lsat_1_v5_gn_6_60760' => 'lsa', 'Lsat_1_v5_gn_8_129201' => 'lsa', 'Lsat_1_v5_gn_8_150301' => 'lsa', 'Lsat_1_v5_gn_8_60761' => 'lsa', 'Lsat_1_v5_gn_8_66640' => 'lsa', 'Lsat_1_v5_gn_9_83300' => 'lsa', 'Manes.01G008300' => 'mes', 'Manes.01G008600' => 'mes', 'Manes.07G141100' => 'mes', 'Manes.07G142750' => 'mes', 'Manes.07G143201' => 'mes', 'Manes.07G144101' => 'mes', 'Manes.13G048000' => 'mes', 'Manes.15G055300' => 'mes', 'Mapoly0045s0011' => 'mpo', 'Mapoly0047s0117' => 'mpo', 'Mapoly0061s0050' => 'mpo', 'Mapoly0179s0014' => 'mpo', 'MBI03_g42549_MAGBIO' => 'mbi', 'MBI06_g27434_MAGBIO' => 'mbi', 'MBI07_g41260_MAGBIO' => 'mbi', 'MBI11_g09536_MAGBIO' => 'mbi', 'MBI14_g29293_MAGBIO' => 'mbi', 'MBI15_g01604_MAGBIO' => 'mbi', 'MBI15_g16939_MAGBIO' => 'mbi', 'MCO05G585' => 'mco', 'MCO07G547' => 'mco', 'MCO09G780' => 'mco', 'MCO10G398' => 'mco', 'MD01G1168000' => 'mdo', 'MD03G1140600' => 'mdo', 'MD04G1013000' => 'mdo', 'MD04G1013400' => 'mdo', 'MD05G1172700' => 'mdo', 'MD07G1234000' => 'mdo', 'MD10G1160800' => 'mdo', 'MD10G1160900' => 'mdo', 'MD10G1161000' => 'mdo', 'MD11G1171300' => 'mdo', 'Medtr3g093870' => 'mtr', 'Medtr4g040350' => 'mtr', 'Medtr4g077700' => 'mtr', 'Medtr4g122580' => 'mtr', 'Medtr4g122620' => 'mtr', 'MELO3C003269.2' => 'cme', 'MELO3C019532.2' => 'cme', 'MELO3C020154.2' => 'cme', 'MELO3C020358.2' => 'cme', 'Migut.F00609' => 'egut', 'Migut.G00631' => 'egut', 'Migut.G00791' => 'egut', 'Migut.G01113' => 'egut', 'Migut.O00219' => 'egut', 'MSTRG.168' => 'ama', 'MSTRG.4233' => 'ama', 'MSTRG.9256' => 'ama', 'Nitab4.5_0000094g0120' => 'nta', 'Nitab4.5_0000348g0060' => 'nta', 'Nitab4.5_0000366g0090' => 'nta', 'Nitab4.5_0001070g0010' => 'nta', 'Nitab4.5_0002204g0040' => 'nta', 'Nitab4.5_0002365g0060' => 'nta', 'Nitab4.5_0002889g0080' => 'nta', 'Nitab4.5_0006093g0010' => 'nta', 'Nitab4.5_0009377g0030' => 'nta', 'Nn1g07935' => 'nnu', 'Nn2g10295' => 'nnu', 'Nn2g14202' => 'nnu', 'Nn3g19994' => 'nnu', 'Nn8g41273' => 'nnu', 'Oeu043455.1' => 'oeu', 'Oeu049043.1' => 'oeu', 'Oeu054416.1' => 'oeu', 'Oeu055765.1' => 'oeu', 'Oeu061890.1' => 'oeu', 'Oeu064520.1' => 'oeu', 'Os01g0821800' => 'osa', 'Os04g0303900' => 'osa', 'Os06g0508700' => 'osa', 'Os10g0400100' => 'osa', 'Peaxi162Scf00304g00618' => 'pax', 'Peaxi162Scf00324g00227' => 'pax', 'Peaxi162Scf00423g00134' => 'pax', 'Peaxi162Scf01205g00178' => 'pax', 'PGR042G0781' => 'pgr', 'PGR044G0579' => 'pgr', 'PGR142G4368' => 'pgr', 'PGSC0003DMG400019113' => 'stu', 'PGSC0003DMG400027598' => 'stu', 'PGSC0003DMG400028753' => 'stu', 'Phvul.009G043500' => 'pvu', 'Phvul.011G011700' => 'pvu', 'Phvul.011G020800' => 'pvu', 'Potri.001G317500' => 'ptr', 'Potri.017G000200' => 'ptr', 'Potri.017G057700' => 'ptr', 'Potri.019G058700' => 'ptr', 'Pp3c13_2300' => 'ppa', 'Pp3c15_24000' => 'ppa', 'Pp3c1_5820' => 'ppa', 'Pp3c25_15060' => 'ppa', 'Pp3c3_5590' => 'ppa', 'PRCOL_00001704' => 'pco', 'PRCOL_00004245' => 'pco', 'PRCOL_00004649' => 'pco', 'PRCOL_00006676' => 'pco', 'Prupe.1G159500' => 'ppe', 'Prupe.2G130000' => 'ppe', 'Prupe.2G130800' => 'ppe', 'Prupe.2G264400' => 'ppe', 'Prupe.6G126300' => 'ppe', 'Prupe.8G200100' => 'ppe', 'Psat0s2557g0040' => 'psa', 'Psat1g168480' => 'psa', 'Psat4g022000' => 'psa', 'Psat4g136360' => 'psa', 'Psat5g068280' => 'psa', 'Psat5g068320' => 'psa', 'Psat5g104120' => 'psa', 'Psat7g142400' => 'psa', 'Psat7g142560' => 'psa', 'Psat7g171920' => 'psa', 'PSO339G1617' => 'pso', 'PSO339G2903' => 'pso', 'PSO339G5039' => 'pso', 'PSO384G1210' => 'pso', 'PSO384G4419' => 'pso', 'PSO541G0555' => 'pso', 'PSO675G0811' => 'pso', 'QL02p084624' => 'qlo', 'QL06p015315' => 'qlo', 'QL08p064889' => 'qlo', 'QL09p052106' => 'qlo', 'QL09p052979' => 'qlo', 'QL10p064653' => 'qlo', 'QL10p065209' => 'qlo', 'QL10p065779' => 'qlo', 'RcHm_v2.0_Chr1g0332211' => 'rch', 'RcHm_v2.0_Chr1g0332221' => 'rch', 'RcHm_v2.0_Chr1g0372341' => 'rch', 'RcHm_v2.0_Chr2g0084251' => 'rch', 'RcHm_v2.0_Chr2g0166871' => 'rch', 'RcHm_v2.0_Chr4g0414261' => 'rch', 'RcHm_v2.0_Chr4g0414311' => 'rch', 'RcHm_v2.0_Chr4g0442441' => 'rch', 'RcHm_v2.0_Chr4g0442451' => 'rch', 'RcHm_v2.0_Chr4g0445731' => 'rch', 'Rhsim02G0168300' => 'rsi', 'Rhsim02G0172200' => 'rsi', 'Rhsim03G0152900' => 'rsi', 'Sabra16G0200900' => 'sbr', 'Sabra17G0005100' => 'sbr', 'Sabra17G0050800' => 'sbr', 'Sabra19G0074000' => 'sbr', 'SalBow3G0802' => 'sbo', 'SalBow3G2409' => 'sbo', 'SalBow3G3036' => 'sbo', 'SalBow3G3488' => 'sbo', 'SalBow8G1842' => 'sbo', 'SalBow8G3376' => 'sbo', 'Sc11g0005860' => 'sci', 'Sc13g0000260' => 'sci', 'Sc19g0007320' => 'sci', 'Sc25g0002320' => 'sci', 'Sed0003636' => 'sed', 'Sed0004820' => 'sed', 'Sed0020246' => 'sed', 'Sed0027305' => 'sed', 'SEGI_14061' => 'sgi', 'SEGI_18038' => 'sgi', 'SEGI_18693' => 'sgi', 'SGA_v2.0_scaffold163G38069' => 'sas', 'SGA_v2.0_scaffold286G47137' => 'sas', 'SGA_v2.0_scaffold299G47730' => 'sas', 'SGA_v2.0_scaffold44G16623' => 'sas', 'SHI11900' => 'shi', 'SHI28911' => 'shi', 'SHI28912' => 'shi', 'SMO171G0122' => 'smo', 'SMO351G0054' => 'smo', 'SMO353G0071' => 'smo', 'SMO364G0158' => 'smo', 'Solyc06g048610.3' => 'sly', 'Solyc08g015960.3' => 'sly', 'Sopen00g013420' => 'spe', 'Sopen06g014800' => 'spe', 'Sopen07g004890' => 'spe', 'Sopen08g006220' => 'spe', 'Sp4g22990' => 'spa', 'Sp5g03200' => 'spa', 'Sp7g11570' => 'spa', 'TAR362G0810' => 'tar', 'TAR622G0405' => 'tar', 'TAR623G1554' => 'tar', 'TAR633G0494' => 'tar', 'THA.LOC104802526' => 'tha', 'THA.LOC104802529' => 'tha', 'THA.LOC104803210' => 'tha', 'THA.LOC104804806' => 'tha', 'THA.LOC104808703' => 'tha', 'Thecc.04G199200' => 'tca', 'Thecc.10G176400' => 'tca', 'Thecc.10G179100' => 'tca', 'Thecc.10G189200' => 'tca', 'Thhalv10006155m.g' => 'esa', 'Thhalv10016505m.g' => 'esa', 'Thhalv10024450m.g' => 'esa', 'TPR.G16116' => 'tpr', 'TPR.G23230' => 'tpr', 'TPR.G25404' => 'tpr', 'TPR.G30170' => 'tpr', 'TPR.G30183' => 'tpr', 'TPR.G34293' => 'tpr', 'TWI12G1242' => 'twi', 'TWI18G0923' => 'twi', 'TWI73G1243' => 'twi', 'unitig_0.g2410' => 'ugi', 'unitig_32.g10864' => 'ugi', 'unitig_578.g16605' => 'ugi', 'vmacro02776' => 'vma', 'vmacro06895' => 'vma', 'vmacro10997' => 'vma', 'vmacro10998' => 'vma', 'vmacro11026' => 'vma', 'VMungo1127G0354' => 'vmu', 'VMungo1127G1164' => 'vmu', 'VMungo1309G2214' => 'vmu', 'VMungo1309G2858' => 'vmu', 'Zm00001eb008700' => 'zma', 'Zm00001eb189910' => 'zma', 'Zm00001eb368820' => 'zma', 'Zm00001eb400100' => 'zma', 'Zm00001eb419200' => 'zma' ) $gf_id = 'HOM05D001184' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001184' ) $data_identifier = 'HOM05D001184' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 8, 'aag' => (int) 9, 'ach' => (int) 8, 'amhyb' => (int) 8, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 5, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 2, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 8, 'han' => (int) 7, 'cav' => (int) 7, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 8, 'lja' => (int) 3, 'lsa' => (int) 11, 'mes' => (int) 8, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 4, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 10, 'pso' => (int) 7, 'qlo' => (int) 8, 'rch' => (int) 10, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 2, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb419200' $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